| bwa_index |
2 |
- data/GCA_002873125.1_ASM287312v1_genomic.fna.amb
- data/GCA_002873125.1_ASM287312v1_genomic.fna
- data/GCA_002873275.1_ASM287327v1_genomic.fna.amb
- data/GCA_002873275.1_ASM287327v1_genomic.fna
|
|
|
| multiqc_raw |
1 |
- analysis/fastqc_raw/multiqc_report.html
|
|
|
| freebayes |
2 |
- analysis/freebayes/12NC29_all.vcf
- analysis/freebayes/12SD80_all.vcf
|
|
|
| index |
2 |
- data/GCA_002873125.1_ASM287312v1_genomic.fna.fai
- data/GCA_002873275.1_ASM287327v1_genomic.fna.fai
|
|
|
| multiqc_trim |
1 |
- analysis/fastqc_trimmed/multiqc_report.html
|
|
|
| fastqc_raw |
4 |
- analysis/fastqc_raw/15FL1-2_R1.small_fastqc.zip
- analysis/fastqc_raw/15Fl1-4_R1.small_fastqc.zip
- analysis/fastqc_raw/15Fl1-4_R2.small_fastqc.zip
- analysis/fastqc_raw/15FL1-2_R2.small_fastqc.zip
|
|
|
| markdup |
4 |
- analysis/bwa_filtered/12NC29/15FL1-2_30MAPQ_RG_mdup.bam
- analysis/bwa_filtered/12NC29/15Fl1-4_30MAPQ_RG_mdup.bam
- analysis/bwa_filtered/12SD80/15FL1-2_30MAPQ_RG_mdup.bam
- analysis/bwa_filtered/12SD80/15Fl1-4_30MAPQ_RG_mdup.bam
|
|
|
| fastqc_trim |
4 |
- analysis/fastqc_trimmed/15Fl1-4_R2_trim_fastqc.zip
- analysis/fastqc_trimmed/15FL1-2_R2_trim_fastqc.zip
- analysis/fastqc_trimmed/15Fl1-4_R1_trim_fastqc.zip
- analysis/fastqc_trimmed/15FL1-2_R1_trim_fastqc.zip
|
|
|
| bam_sort |
4 |
- analysis/bwa_filtered/12NC29/15FL1-2_30MAPQ_RG_sorted.bam
- analysis/bwa_filtered/12NC29/15Fl1-4_30MAPQ_RG_sorted.bam
- analysis/bwa_filtered/12SD80/15FL1-2_30MAPQ_RG_sorted.bam
- analysis/bwa_filtered/12SD80/15Fl1-4_30MAPQ_RG_sorted.bam
|
|
|
| trimmomatic |
2 |
- analysis/trimmed/15Fl1-4_R1_trim.fastq.gz
- analysis/trimmed/15Fl1-4_R2_trim.fastq.gz
- analysis/trimmed/15Fl1-4_R1_trim.unpaired.fastq.gz
- analysis/trimmed/15Fl1-4_R2_trim.unpaired.fastq.gz
- analysis/trimmed/15FL1-2_R1_trim.fastq.gz
- analysis/trimmed/15FL1-2_R2_trim.fastq.gz
- analysis/trimmed/15FL1-2_R1_trim.unpaired.fastq.gz
- analysis/trimmed/15FL1-2_R2_trim.unpaired.fastq.gz
|
|
|
| read_groups |
4 |
- analysis/bwa_filtered/12NC29/15FL1-2_30MAPQ_RG.bam
- analysis/bwa_filtered/12NC29/15Fl1-4_30MAPQ_RG.bam
- analysis/bwa_filtered/12SD80/15FL1-2_30MAPQ_RG.bam
- analysis/bwa_filtered/12SD80/15Fl1-4_30MAPQ_RG.bam
|
|
|
| map_filter |
4 |
- analysis/bwa_filtered/12NC29/15FL1-2_30MAPQ.bam
- analysis/bwa_filtered/12NC29/15Fl1-4_30MAPQ.bam
- analysis/bwa_filtered/12SD80/15FL1-2_30MAPQ.bam
- analysis/bwa_filtered/12SD80/15Fl1-4_30MAPQ.bam
|
|
|
| sam_to_bam |
4 |
- analysis/bwa/12NC29/15FL1-2.bam
- analysis/bwa/12NC29/15Fl1-4.bam
- analysis/bwa/12SD80/15FL1-2.bam
- analysis/bwa/12SD80/15Fl1-4.bam
|
|
|
| bwa_mem |
4 |
- analysis/bwa/12NC29/15FL1-2.sam
- analysis/bwa/12NC29/15Fl1-4.sam
- analysis/bwa/12SD80/15FL1-2.sam
- analysis/bwa/12SD80/15Fl1-4.sam
|
|
|